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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/RingsCountDescriptors.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,138 @@ +<html> +<head> +<title>MayaChemTools:Documentation:MolecularDescriptors::RingsCountDescriptors.pm</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<tr align="left" valign="top"><td width="33%" align="left"><a href="./MolecularVolumeDescriptors.html" title="MolecularVolumeDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./RotatableBondsDescriptors.html" title="RotatableBondsDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>MolecularDescriptors::RingsCountDescriptors.pm</strong></td><td width="33%" align="right"><a href="././code/RingsCountDescriptors.html" title="View source code">Code</a> | <a href="./../pdf/RingsCountDescriptors.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/RingsCountDescriptors.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/RingsCountDescriptors.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/RingsCountDescriptors.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>RingsCountDescriptors</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>use MolecularDescriptors::RingsCountDescriptors;</p> +<p>use MolecularDescriptors::RingsCountDescriptors qw(:all);</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p><strong>RingsCountDescriptors</strong> class provides the following methods:</p> +<p> <a href="#new">new</a>, <a href="#generatedescriptors">GenerateDescriptors</a>, <a href="#getdescriptornames">GetDescriptorNames</a>, <a href="#stringifyringscountdescriptors">StringifyRingsCountDescriptors</a> +</p><p><strong>RingsCountDescriptors</strong> is derived from <strong>MolecularDescriptors</strong> class which in turn +is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined +in <strong>RingsCountDescriptors</strong>, <strong>MolecularDescriptors</strong> or <strong>ObjectProperty</strong> classes using Perl's +AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:</p> +<div class="OptionsBox"> + Set<PropertyName>(<PropertyValue>); +<br/> $PropertyValue = Get<PropertyName>(); +<br/> Delete<PropertyName>();</div> +<p><strong>RingsCountDescriptors</strong> class doesn't perform any ring or aromaticity detection before +counting their number in a molecule. Instead, it assumes ring and aromaticity detection have +been performed by caller using <strong>DetectRings</strong> [Ref 31] and <strong>DetectAromaticity</strong> methods +available in <strong>Molecule</strong>.</p> +<p><strong>DetectAromaticity</strong> method available in <strong>Molecule</strong> class assigns aromaticity to rings +using Huckel rule as explained below:</p> +<p>o Ring aromaticity is determined using Huckel's rule: a ring containing 4n + 2 pi electrons is +considered aromatic.</p> +<p>o Hetrocyclic rings containing N, O and S atoms fall into two classes: Basic aromatic and +Non-basic aromatic. In Basic aromatic hetrocyclic rings, heteroatom itself is involved in a +double bond. (e.g. Pyridine) However, in non-basic hetrocyclic rings, heteroatom might have +an attached hydrogen atom and the remaining lone pair contribute to electron delocalization +and contributes to 4n + 2 electrons. (e.g. Pyrrole, Furan)</p> +<p>o For molecules containing fused rings, each fused ring set is considered as one aromatic +system for counting pi electrons to satisfy Huckel's rule; In case of a failure, rings in +fused set are treated individually for aromaticity detection. Additionally, non-fused +rings are handled on their own during aromaticity detection.</p> +<p> +</p> +<h2>METHODS</h2> +<dl> +<dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NewRingsCountDescriptors = new MolecularDescriptors:: + RingsCountDescriptors( + %NamesAndValues);</div> +<p>Using specified <em>RingsCountDescriptors</em> property names and values hash, <strong>new</strong> +method creates a new object and returns a reference to newly created <strong>RingsCountDescriptors</strong> +object. By default, the following properties are initialized:</p> +<div class="OptionsBox"> + Molecule = '' +<br/> Type = 'RingsCount'</div> +<div class="OptionsBox"> + @DescriptorNames = ('Rings', 'AromaticRings') +<br/> @DescriptorValues = ('None', 'None')</div> +<p>Examples:</p> +<div class="OptionsBox"> + $RingsCountDescriptors = new MolecularDescriptors::RingsCountDescriptors( + 'Molecule' => $Molecule);</div> +<div class="OptionsBox"> + $RingsCountDescriptors = new MolecularDescriptors::RingsCountDescriptors();</div> +<div class="OptionsBox"> + $RingsCountDescriptors->SetMolecule($Molecule); +<br/> $RingsCountDescriptors->GenerateDescriptors(); +<br/> print "RingsCountDescriptors: $RingsCountDescriptors\n";</div> +</dd> +<dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $RingsCountDescriptors->GenerateDescriptors();</div> +<p>Calculate number of rings and aromatic rings in a molecule and returns +<em>RingsCountDescriptors</em>.</p> +</dd> +<dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @DescriptorNames = $RingsCountDescriptors->GetDescriptorNames(); +<br/> @DescriptorNames = MolecularDescriptors::RingsCountDescriptors:: + GetDescriptorNames();</div> +<p>Returns all available descriptor names as an array.</p> +</dd> +<dt><strong><a name="stringifyringscountdescriptors" class="item"><strong>StringifyRingsCountDescriptors</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $String = $RingsCountDescriptors-> + StringifyRingsCountDescriptors();</div> +<p>Returns a string containing information about <em>RingsCountDescriptors</em> object.</p> +</dd> +</dl> +<p> +</p> +<h2>AUTHOR</h2> +<p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> +<p> +</p> +<h2>SEE ALSO</h2> +<p><a href="./MolecularDescriptors.html">MolecularDescriptors.pm</a>, <a href="./MolecularDescriptorsGenerator.html">MolecularDescriptorsGenerator.pm</a> +</p> +<p> +</p> +<h2>COPYRIGHT</h2> +<p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> +<p>This file is part of MayaChemTools.</p> +<p>MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the GNU Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.</p> +<p> </p><p> </p><div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<tr align="left" valign="top"><td width="33%" align="left"><a href="./MolecularVolumeDescriptors.html" title="MolecularVolumeDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./RotatableBondsDescriptors.html" title="RotatableBondsDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>MolecularDescriptors::RingsCountDescriptors.pm</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>